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Yorodumi- PDB-8th8: Linker domain of Nexin-dynein regulatory complex from Tetrahymena... -
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-Basic information
Entry | Database: PDB / ID: 8th8 | |||||||||
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Title | Linker domain of Nexin-dynein regulatory complex from Tetrahymena thermophila | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / nexin-dynein regulatory complex / cilia / axoneme / dynein | |||||||||
Function / homology | Function and homology information regulation of cilium movement / axonemal dynein complex assembly / sperm axoneme assembly / cytoskeletal motor regulator activity / axonemal dynein complex / sperm principal piece / cilium-dependent cell motility / regulation of Arp2/3 complex-mediated actin nucleation / flagellated sperm motility / actomyosin structure organization ...regulation of cilium movement / axonemal dynein complex assembly / sperm axoneme assembly / cytoskeletal motor regulator activity / axonemal dynein complex / sperm principal piece / cilium-dependent cell motility / regulation of Arp2/3 complex-mediated actin nucleation / flagellated sperm motility / actomyosin structure organization / myosin II complex / motile cilium / locomotion / myosin heavy chain binding / axoneme / mitotic cytokinesis / cilium assembly / sperm flagellum / ciliary basal body / post-embryonic development / cell motility / cilium / small GTPase binding / cell migration / lamellipodium / microtubule binding / microtubule / cytoskeleton / calcium ion binding / Golgi apparatus / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Tetrahymena thermophila (eukaryote) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.4 Å | |||||||||
Authors | Ghanaeian, A.G. / Bui, K.H. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Integrated modeling of the Nexin-dynein regulatory complex reveals its regulatory mechanism. Authors: Avrin Ghanaeian / Sumita Majhi / Caitlyn L McCafferty / Babak Nami / Corbin S Black / Shun Kai Yang / Thibault Legal / Ophelia Papoulas / Martyna Janowska / Melissa Valente-Paterno / Edward ...Authors: Avrin Ghanaeian / Sumita Majhi / Caitlyn L McCafferty / Babak Nami / Corbin S Black / Shun Kai Yang / Thibault Legal / Ophelia Papoulas / Martyna Janowska / Melissa Valente-Paterno / Edward M Marcotte / Dorota Wloga / Khanh Huy Bui / Abstract: Cilia are hairlike protrusions that project from the surface of eukaryotic cells and play key roles in cell signaling and motility. Ciliary motility is regulated by the conserved nexin-dynein ...Cilia are hairlike protrusions that project from the surface of eukaryotic cells and play key roles in cell signaling and motility. Ciliary motility is regulated by the conserved nexin-dynein regulatory complex (N-DRC), which links adjacent doublet microtubules and regulates and coordinates the activity of outer doublet complexes. Despite its critical role in cilia motility, the assembly and molecular basis of the regulatory mechanism are poorly understood. Here, using cryo-electron microscopy in conjunction with biochemical cross-linking and integrative modeling, we localize 12 DRC subunits in the N-DRC structure of Tetrahymena thermophila. We also find that the CCDC96/113 complex is in close contact with the DRC9/10 in the linker region. In addition, we reveal that the N-DRC is associated with a network of coiled-coil proteins that most likely mediates N-DRC regulatory activity. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8th8.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8th8.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 8th8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/8th8 ftp://data.pdbj.org/pub/pdb/validation_reports/th/8th8 | HTTPS FTP |
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-Related structure data
Related structure data | 41251MC 8tekC 8tidC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Dynein regulatory complex protein ... , 3 types, 3 molecules AJK
#1: Protein | Mass: 98840.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q229S1 |
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#10: Protein | Mass: 44990.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23S05 |
#11: Protein | Mass: 51315.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: A4VD15 |
-Protein , 10 types, 13 molecules BCFGHIiLPQRSs
#2: Protein | Mass: 60596.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24DJ0 | ||||||||
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#3: Protein | Mass: 68009.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MG46 | ||||||||
#6: Protein | Mass: 52938.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24C31 | ||||||||
#7: Protein | Mass: 39706.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24CL2 | ||||||||
#8: Protein | Mass: 101225.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MLZ4 | ||||||||
#9: Protein | Mass: 22062.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: W7WX86 #12: Protein | | Mass: 101144.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LWE3 #13: Protein | | Mass: 94540.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M6D6 #14: Protein | Mass: 23862.807 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MDA9 #15: Protein | Mass: 22170.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22RH5 |
-Growth-arrest-specific microtubule-binding ... , 2 types, 2 molecules DE
#4: Protein | Mass: 56190.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LT80 |
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#5: Protein | Mass: 55393.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23YW7 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Linker domain of Nexin-dynein regulatory complex from Tetrahymena thermophila Type: CELL / Entity ID: #14, #3-#7, #9-#13, #1-#2, #15 / Source: NATURAL |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.19.2_4158: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 7.4 Å / Resolution method: OTHER / Num. of particles: 211502 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 0 Å2 | ||||||||||||||||||||||||
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